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SRZ2961006 Sample ID 1774
| Paper identifier | Magnuson2015identifying |
| SRP accession | SRP066673 |
| GEO accession | GSE75398 |
| Samples | SRR2961006 |
| SRR2961007 |
| QC score | 4 |
| Replicate | 1 |
| Protocol | Bru-seq |
| Library prep | ligation |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | reverse |
| Reverse complemented? | True |
| Mapped strandedness | forward |
| Timecourse | False |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | |
| Stranded gene read counts | TXT file | |
| Unstranded bidirectional read counts | TXT file | |
| Tfit bidirectional regions | BED file | |
| dREG bidirectional regions | BED file | |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | HF1 |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | bromouridine (2 mM) | -30 min | 0 min | 30 min |
| treatment | ultraviolet C (1 J/m^2/s) | -1820 s | -1800 s | 20 s |
| treatment | TNF-alpha (10 ng/mL) | -90 min | -30 min | 1 hr |
| Pipeline info and software versions | |
| Sample notes | Bru-seq; replicate information unclear, but points toward technical replicates |
| Analysis notes |
| Sample QC score | 4 |
| Sample NRO score | 2 |
| Raw read length | 52 |
| Read depth after trimming | 53,335,926 |
| Duplication proportion | 0.87091 |
| Proportion reads mapped | 0.9419 |
| Exon/intron ratio | 2.91734 |
| Unique read proportion | 0.31666 |
| Total # Tfit bidirectionals | 13448 |
| # Promoter Tfit bidirectionals | 2563 |
| # Intronic Tfit bidirectionals | 8384 |
| # Intergenic Tfit bidirectionals | 1915 |
| Total # dREG bidirectionals | 8915 |
| # Promoter dREG bidirectionals | 2049 |
| # Intronic dREG bidirectionals | 5570 |
| # Intergenic dREG bidirectionals | 1434 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |